Aiida-vibroscopy: Is it possible to access vibration modes?

New to AiiDA
1

Hi @bastonero

Is it possible to access the vibrational modes from vibroscopy, like we do in ph.x (.axsf file)?

Rijan

2

I don’t know this format. What do you mean? You can use one of the scripts I shared, and use the Phonopy class to post-process further.

3

Hi @bastonero
I am talking about how atoms vibrates in each mode (that also includes in Raman active modes) kind of display. I havent used phonopy a lot, but can something like this (eigenvectors in each modes) be extracted from calculation completed in IRamanSpectraWorkChain?

Capture

4

Unfortunately there is no direct way to get such thing yet. Since the entire aiida-vibroscopy is built on top of Phonopy, you should look into it to get these.

So for instace, via aiida-phonopy:

from aiida_phonopy.calculations.phonopy import PhonopyCalculation

inputs = {
  'parameters': Dict('anime_type': 'jmol', 'anime': [0,0,0]), # phonons at Gamma
  'force_constants': vibrational_data_node, # here a vibrational data node that you want to use
  'code': load_code('phonopy@localhost'), # change here
  'settings': Dict('keep_animation_files': True).
}

calc = submit(PhonopyCalculation, **inputs)

print(f'Launched calculation with PK = {calc.pk}')

Then you can find these files in calc.outputs.retrieved (or just do load_node(PK).outputs.retrieved). This is a FolderData, and then via python you can simply get the file and dump it wherever you want.
If you want other options look here: Setting tags — Phonopy v.2.22.0
You can use any of such setting tags to postprocess your data.

For instance:

node = load_node(PK)
folder = node.outputs.retrieved

print(folder.list_object_names())

You can see how to use FolderData here: Data types — AiiDA 2.5.1.post0 documentation

Bare with me if some typos are in the scripts, just wrote them on the fly. But you should have got the gist.

5

Hi Lorenzo,
Is this a separate independent run or dependent on previous IRamanSpectraWorkChain?
Based on this input, how will phonopy know what structure/material I am talking about?

6

You need to provide the force_constants input. The VibrationalData contains such information. So just put such a node which is an output of the IRamanSpectraWorkChain.
E.g.

...
'force_constants': load_node(PK).outputs.vibrational_data.numerical_accuracy_2, 
...

where PK is of the IRamanSpectraWorkChain finished correctly

7

Understood.

I am trying to create code for phonopy so that I could load code in the inputs above. Below is the code.yaml file but I am not sure what would be the default_calc_job_plugin: ?

label: 'phonopy'
description: 'Phonopy'
default_calc_job_plugin: ' '
filepath_executable: '/users/rkarkee/phonopy'
computer: 'newhpc'
8

you can also use your local version of phonopy, as it is a simple post-process. for instructions: Get started — aiida-phonopy 1.1.4 documentation

9

In this part, I got this syntax error:

(aiidaENV) rkarkee@ch-fe2:~> python displacement.py
  File "/users/rkarkee/displacement.py", line 12
    'settings': orm.Dict('keep_animation_files': True)
                                               ^
SyntaxError: invalid syntax

My displacement.py is:

from aiida_phonopy.calculations.phonopy import PhonopyCalculation
from aiida import load_profile, orm
from aiida.engine import submit

code = orm.load_code('phonopy@newhpc')
parameters={'anime_type': 'jmol', 'anime': [0,0,0]}

inputs = {
  'code': code,
  'parameters': orm.Dict(parameters),
  'force_constants': load_node(2418).outputs.vibrational_data.numerical_accuracy_4, # here a vibrational data node that you want to use
  'settings': orm.Dict('keep_animation_files': True)
}

calc = submit(PhonopyCalculation, **inputs)

print(f'Launched calculation with PK = {calc.pk}')
10

Hello, you simply missed to insert {…}.